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iRNA-COSI
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APAeval
Community effort to evaluate computational methods for the detection and quantification of poly(A) sites and estimating their differential usage across RNA-seq samples
MIT License
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docs: comment on filtering before OEB upload
#471
ninsch3000
closed
8 months ago
0
docs: add jmfernandez as a contributor for ideas, infra, and mentoring
#470
allcontributors[bot]
closed
1 year ago
1
docs: add missing contributors
#469
ninsch3000
closed
1 year ago
0
feat(Summary workflow): additional annotation dependent metrics
#468
ninsch3000
opened
1 year ago
0
chore: migrate containers from dockerhub.io/apaeval to biocontainers
#467
ninsch3000
opened
1 year ago
0
Docs: from hackathon version to publication ready
#464
ninsch3000
closed
1 year ago
1
fix: remove `event_date` from SWFs
#463
ninsch3000
closed
1 year ago
0
fix: Update OEB event Ids in SWFs
#462
ninsch3000
closed
1 year ago
0
fix: remove AUC metric
#461
ninsch3000
closed
1 year ago
0
fix: make SWF output jsons OEB compatible
#460
ninsch3000
closed
1 year ago
2
SWF: make output jsons OEB compatible
#459
ninsch3000
closed
1 year ago
1
feat(Summary workflow): check that PAS are reported as single nucleotide in input bed
#458
ninsch3000
opened
1 year ago
0
feat(Execution workflows / Utils): making RefSeq annotations work for QAPA and PAQR.
#457
mrgazzara
opened
1 year ago
3
chore: remove unnecessary requirement in identification swf
#456
dominikburri
opened
1 year ago
0
pyranges in utils/apaeval setup
#455
ninsch3000
closed
1 year ago
0
fix: filter on score only after matched modifications
#454
dominikburri
closed
1 year ago
0
fix: deal with empty matched df
#453
dominikburri
closed
1 year ago
0
fix: swf-ident: reduce memory and time consumption
#452
dominikburri
closed
1 year ago
0
Execution workflow: GETUTR - report Format 04 BED file in workflow (per-PAS fractional relative usage)
#451
faricazjj
closed
1 year ago
0
Execution workflow: GETUTR - report Format 04 BED file in workflow (per-PAS fractional relative usage)
#450
faricazjj
closed
1 year ago
0
Fix: scikit-learn instead of sklearn
#449
ninsch3000
closed
1 year ago
0
feat: SWF: identification metric nr. 5
#448
dominikburri
closed
1 year ago
0
Fix: SWF challenge selection
#447
ninsch3000
closed
1 year ago
0
Fix: utils metrics2tsv to work for identification event
#446
ninsch3000
closed
1 year ago
0
Ewf bugfix: Change GETUTR challenge output file delimiter from space to tab
#445
SamBryce-Smith
closed
1 year ago
0
SWF: allow multiple challenges per infile
#444
ninsch3000
closed
1 year ago
4
Execution workflow update: enable Singularity option for TAPAS
#443
faricazjj
closed
1 year ago
0
Execution workflow update: enable Singularity option for TAPAS
#442
faricazjj
closed
1 year ago
0
Execution workflow update: IsoSCM doesn't run with reverse_forward and unstranded combination
#441
faricazjj
closed
1 year ago
0
Execution workflow update: IsoSCM doesn't run with reverse_forward and unstranded combination
#440
faricazjj
closed
1 year ago
0
Bug: GETUTR file not found error in postprocessing step when using huge sample file
#439
faricazjj
closed
1 year ago
0
Bug: GETUTR file not found error in postprocessing step when using huge sample file
#438
faricazjj
closed
1 year ago
0
[BugFix] QAPA error converting string "NA" to float when calculating PPAU
#437
faricazjj
closed
1 year ago
3
Bug: QAPA error converting string "NA" to float when calculating PPAU
#436
faricazjj
closed
1 year ago
0
Bug: DaPars file not found error in postprocessing step when using huge sample file
#435
faricazjj
closed
1 year ago
0
[Bug Fix] Dapars file not found error in postprocessing when using big input sample files
#434
faricazjj
closed
1 year ago
0
SWF: include parameter to filter expression
#433
dominikburri
closed
1 year ago
0
SWF: identification annotation based metrics
#432
dominikburri
closed
1 year ago
2
[Bug Fix] IsoSCM identification output should be from assemble step
#431
faricazjj
closed
1 year ago
2
feat: unify TP calculation in aQ swf
#430
dominikburri
closed
1 year ago
0
[Bug Fix] IsoSCM identification output should be from compare step
#429
faricazjj
closed
1 year ago
1
Add filterPAS() function to the apaeval module
#428
yuukiiwa
closed
1 year ago
0
Execution workflow: TAPAS - report Format 04 BED file in workflow (per-PAS fractional relative usage)
#427
faricazjj
closed
1 year ago
0
Execution workflow: TAPAS - report Format 04 BED file in workflow (per-PAS fractional relative usage)
#426
faricazjj
closed
1 year ago
0
SWF: unify true positive calculation
#425
ninsch3000
closed
1 year ago
0
AbsQuant SWF: filter for non-zero expression
#424
ninsch3000
closed
1 year ago
1
Getutr nextflow
#423
grexor
closed
1 year ago
4
functions for relative expression metrics
#422
yuukiiwa
closed
1 year ago
1
SWF: Identification
#421
ninsch3000
closed
1 year ago
1
fix: wrong indentation
#420
ninsch3000
closed
2 years ago
0
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